Robust outlier identification for DNA methylation data

add_ensemble_regulatory | Add ENSEMBL regulatory regions to epimutations |

annotate_cpg | Annotate the DMR resulting from epimutacions package |

annotate_epimutations | Annotate the results of epimutations or... |

AS204 | Algorithm AS 204 |

betas_from_bump | Obtains bumps beta values |

betas_sd_mean | Computes beta values, standard deviation and mean to plot the... |

cols_names | Sets common column names in a data frame |

create_GRanges_class | Generates a GRanges object |

epi_beta | Identifies epimutations based on a beta distribution. |

epi_iForest | Identifies epimutations using Isolation Forest |

epi_mahdist | Identifies epimutations using Robust Mahalanobis distance |

epi_manova | Identifies epimutations using MANOVA |

epi_mlm | Detects epimutations using Multivariate Linear Model (MLM) |

epimutations | Epimutations analysis based on outlier detection methods |

epimutations_one_leave_out | Epimutations analysis based on outlier detection methods |

epi_parameters | Settings for parameters of 'epimutations' and... |

epi_preprocess | Preprocess methylation array |

epi_quantile | Identifies epimutations using quantile distribution |

getBetaParams | Model methylation as a beta distribution |

get_candRegsGR | Candidate regions to be epimutations |

get_ENSEMBL_data | Get ENSEMBL regulatory features overlapping a genomic region |

GRset | GRset |

merge_records | Merge records for the same ENSEMBL regulatory element |

mlm | Non-parametric, Asymptotic P-values for Multivariate Linear... |

mlmtst | Sums of Squares and Pseudo-F Statistics from a Multivariate... |

norm_parameters | Settings for parameters of epi_preprocess function |

p.asympt | Asymptotic P-values |

plot_epimutations | Plot a given epimutation and locate it along the genome |

process_ENSEMBL_results | Process data from ENSEMBL |

res.epi.manova | res.epi.manova |

res_iForest | Creates a data frame containing the results obtained from... |

res_mahdist | Creates a data frame containing the results obtained from... |

res_manova | Creates a data frame containing the results obtained from... |

res_mlm | Creates a data frame containing the results obtained from MLM |

UCSC_annotation | UCSC gene annotations |

UCSC_regulation | UCSC annotation |

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